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Tools for making TxDb objects from genomic annotations

Bioconductor version: Release (3.19)

A set of tools for making TxDb objects from genomic annotations from various sources (e.g. UCSC, Ensembl, and GFF files). These tools allow the user to download the genomic locations of transcripts, exons, and CDS, for a given assembly, and to import them in a TxDb object. TxDb objects are implemented in the GenomicFeatures package, together with flexible methods for extracting the desired features in convenient formats.

Author: H. Pagès [aut, cre], M. Carlson [aut], P. Aboyoun [aut], S. Falcon [aut], M. Morgan [aut], M. Lawrence [ctb], J. MacDonald [ctb], M. Ramos [ctb], S. Saini [ctb], L. Shepherd [ctb]

Maintainer: H. Pagès <hpages.on.github at>

Citation (from within R, enter citation("txdbmaker")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Making TxDb Objects HTML R Script
Reference Manual PDF


biocViews Annotation, DataImport, Genetics, GenomeAnnotation, GenomeAssembly, Infrastructure, Sequencing, Software
Version 1.0.1
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License Artistic-2.0
Depends BiocGenerics, S4Vectors, GenomeInfoDb(>= 1.39.9), GenomicRanges, GenomicFeatures
Imports methods, utils, stats, tools, httr, rjson, DBI, RSQLite (>= 2.0), IRanges, UCSC.utils, AnnotationDbi, Biobase, BiocIO, rtracklayer, biomaRt(>= 2.59.1)
System Requirements
Bug Reports
See More
Suggests RMariaDB, mirbase.db, ensembldb, RUnit, BiocStyle, knitr
Linking To
Depends On Me mygene
Imports Me ASpli, crisprDesign, crisprViz, customProDB, DegNorm, EpiTxDb, FLAMES, GenomicPlot, IntEREst, metaseqR2, ORFik, OrganismDbi, OUTRIDER, proActiv, proBAMr, QuasR, RCAS, recoup, Rhisat2, RiboDiPA, ribosomeProfilingQC, RNAmodR, scanMiRApp, scruff, sitadela, trackViewer, txcutr, tximeta, geneLenDataBase
Suggests Me AnnotationHub, bumphunter, BUSpaRse, DEXSeq, doubletrouble, eisaR, FLAMES, GenomicFeatures, GenomicRanges, raer, recount, SplicingGraphs, SPLINTER, systemPipeR
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package txdbmaker_1.0.1.tar.gz
Windows Binary
macOS Binary (x86_64) txdbmaker_1.0.1.tgz
macOS Binary (arm64) txdbmaker_1.0.1.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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Package Short Url
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Old Source Packages for BioC 3.19 Source Archive